Tophat's bowtie parameters

[deepsea]

Hi folks,

I am using tophat in my RNA-seq of a high polymorphic genome. I think Tophat calls bowtie with '-v 2', but I found many reads with more than 2 mismatches were mapped to the genome. I took one as the test, it has 5 mismatches with good phred quality scores:

13:C>T,27:C>A,38:T>C,57:G>A,64:C>A

Using -v 3, or default -n 2 -l 28 -e 70 cannot map it, but using -n 2 -l 28 -e 150 can map it.

Why can tophat map these kind of reads?

Thanks!

[Gangcai]

I also have a quite similar question: How to set the other bowtie parameters in tophat(such as "-a --best --strata")?

[Xi Wang]

I also have a quite similar question: How to set the other bowtie parameters in tophat(such as "-a --best --strata")?

I did it just by editing the python script of tophat.

[thinkRNA]

I did it just by editing the python script of tophat.

How exactly did you do this? Which line and what is the name of the script?

I appreciate your help in advance. Thanks !

[Gangcai]

you can modify the tophat bin file

The file you should modify is tophat-1.0.13/bin/tophat. I have an example file in the attached file for my question(add --best, --strata and --seedmms)(the modified line have #by gangcai)

After modification, you can run tophat like this:

$tophat --best --strata --seedmms 3 ......

How exactly did you do this? Which line and what is the name of the script?

I appreciate your help in advance. Thanks !

[Xi Wang]

The file you should modify is tophat-1.0.13/bin/tophat. I have an example file in the attached file for my question(add --best, --strata and --seedmms)(the modified line have #by gangcai)

After modification, you can run tophat like this:

$tophat --best --strata --seedmms 3 ......

Great! I think tophat developers should also take those options into consideration.

[peromhc]

I agree, one of the strengths of BOWTIE is being able to modify the way it works via its options- but all of this customizability is lost when using TOPHAT..

[joseph]

help with Tophat's bowtie parameters

The file you should modify is tophat-1.0.13/bin/tophat. I have an example file in the attached file for my question(add --best, --strata and --seedmms)(the modified line have #by gangcai)

After modification, you can run tophat like this:

$tophat --best --strata --seedmms 3 ......

Hi
If it is not too much trouble, can you post a tophat file with modification to the the latest version (1.2). My data maps better when I set my own -n/--seedmms and -l/--seedlen parameters.
As you can tell, I don't know how to write scripts.

Thank you in advance

Joseph Dhahbi

[Xi Wang]

Hi
If it is not too much trouble, can you post a tophat file with modification to the the latest version (1.2). My data maps better when I set my own -n/--seedmms and -l/--seedlen parameters.
As you can tell, I don't know how to write scripts.

Thank you in advance

Joseph Dhahbi

I think the authors of Tophat don't want users to run Tophat in this way. One of the reasons should be that those parameters also apply to segment mapping in Tophat. A segment is an arbitrary part of a read, not necessarily from the left end of a read. So the seed region of a segment could be different from the seed of a whole read. This may cause some biases, I guess.

[shrutiisarda]

TopHat source code modification to include --best

Hi all,

I want to use TopHat for my mRNA Seq analysis, but I am unable to include --best..

I tried modifying the code to include best (similar to what's given above), but I was not successful..

Could someone please provide a modification in the latest version (1.3.1)? *I wish tophat did not make it impossible to edit bowtie options on the command line*

[blue mood]

i have another problem about tophat.
i mapped 90bp pair-end reads twice with tophat of different versions with same arguments -g 10 -r 20 --solexa1.3-quals .The default segment-mismatch is 2. in the otput of the older version(1.0.12),the minimum match length is 75bp,why?. in the output of the latest version(1.3.1) it is mostly 90bp, is it because the -v 2 ?
is there anyone facing the same problem?

[DineshCyanam]

Shrutii,
U can try a different approach... Might work... If u have already run tophat... there is a log folder in the output directory. Open run.log file. It lists the sequence of commands tophat executes... I think there are 29 steps totally. U can modify the steps in which bowtie is called and give the --best flag... and then run all the commands as a bash script but as Xi Wang mentioned above, I too feel Cole or the other authors of Tophat do not want users to run it this way. I might be wrong tho...

Dinesh

Hi all,

I want to use TopHat for my mRNA Seq analysis, but I am unable to include --best..

I tried modifying the code to include best (similar to what's given above), but I was not successful..

Could someone please provide a modification in the latest version (1.3.1)? *I wish tophat did not make it impossible to edit bowtie options on the command line*